Combine harvesters are provided with a processing system comprising a thresher rotor assembly and cleaning system. The thresher rotor assembly typically comprises a thresher rotor or cylinder and one or more arcuate, foraminous concaves and separator grate assemblies, through which crop material threshed by the thresher rotor pass to the cleaning system. The threshed crop material may comprise kernels of grain, chaff, small pieces of stalk or straw, etc. The cleaning system is used to remove chaff and other residue from, for instance, the threshed grain. Within the cleaning system, an oscillating grain or cascade pan and sieve assemblies of a shaker shoe assembly (hereinafter, also simply shoe) in conjunction with air flow remove the chaff from the threshed grain. The cleaned grain is conveyed to a discharge auger that elevates the grain to an onboard storage bin, whereas material other than grain (or MOG) and possibly unthreshed grain is directed over the edge of a bottom sieve assembly of the shoe to a different discharge outlet for recirculation back through the thresher rotor assembly and cleaning system to extract any unthreshed grain. A fan of the cleaning system produces an airstream through the shoe that entrains the lighter non-grain particles and carries them out the rear of the combine harvester. The versatility of the combine harvester enables harvesting of many different crops under a variety of conditions. In turn, the variability in crops and conditions may provide challenges to combine harvester operations that affect the capacity of the shoe.